rs11205449

Variant names:

• chr1-48181452-T-G
• rs11205449
• ENST00000431986.2:n.248+8233T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431986.2(ENSG00000223720):​n.248+8233T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,050 control chromosomes in the GnomAD database, including 6,268 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (6268 hom., cov: 31)
• Consequence: ENSG00000223720 ENST00000431986.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402
• Publications: 4 publications found

Genes affected

ENSG00000223720 (HGNC:):

SKINT1L (HGNC:33993): (Skint1 like (pseudogene))

LINC02794 (HGNC:54318): (long intergenic non-protein coding RNA 2794)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431986.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SKINT1L	NR_026749.2		n.117+259A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223720	ENST00000431986.2	TSL:3	n.248+8233T>G		intron	N/A
	ENSG00000290466	ENST00000706231.2		n.117+259A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39811 AN: 151932 Hom.: 6266 Cov.: 31

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.262

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.262 AC: 39802 AN: 152050 Hom.: 6268 Cov.: 31 AF XY: 0.264 AC XY: 19596 AN XY: 74316

African (AFR) AF: 0.0832 AC: 3453 AN: 41506

American (AMR) AF: 0.246 AC: 3763 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1426 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1965 AN: 5134

South Asian (SAS) AF: 0.343 AC: 1646 AN: 4804

European-Finnish (FIN) AF: 0.315 AC: 3330 AN: 10570

Middle Eastern (MID) AF: 0.403 AC: 117 AN: 290

European-Non Finnish (NFE) AF: 0.342 AC: 23278 AN: 67978

Other (OTH) AF: 0.260 AC: 549 AN: 2110

Alfa AF: 0.302 Hom.: 14482

Bravo AF: 0.249

Asia WGS AF: 0.351 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.2
DANN	Benign	0.63
PhyloP100		0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11205449; hg19: chr1-48647124;